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A battle with Petey Piranha in Boss Battles Mode. Note that the cages are empty, and the sky is blue, like in The Great Maze.

The goal of Boss Battles Mode is to defeat every boss in the game with a single stock. When a player begins Boss Battles Mode, they are immediately dropped into combat against one of nine bosses (exluding Tabuu). Once a boss is defeated, the player is brought to the rest area. The rest area displays all defeated bosses as trophies, a screen that displays the face of next boss to be fought, and has limited recovery items. There are three Heart Containers, which recover the player's damage to 0% and don't reappear upon later visits to the rest area. This format continues until all bosses are defeated. The bosses are fought in random order, except for Tabuu, who is always last.

This format is mostly the same as All-Star Mode. However, continues are unavailable, so the mode must be retried from the beginning if a Game Over is earned. The final three bosses before Tabuu move and attack at a faster rate (most noticeable with Rayquaza & Galleom), and boss HP gradually increases as the mode progresses. The player is treated to a picture of one of the bosses upon completing the mode; this picture varies depending on the difficulty level chosen.

Boss Battles also includes a co-op mode, where both characters will have a single stock and there will be three extra Heart Containers for a total of six. Both players must remain alive; if either player loses their stock, the game ends.

Several of the bosses are slightly altered from their appearances in other modes.

Bosses generally have around half the HP they do in the equivalent difficulty in SSE and Classic Mode, with their attacks having about half the power as well. This may be to compensate for stickers being unavailable.

Bosses are additionally slower than normal, unless they're one of the final three before Tabuu.

Crazy Hand is a boss on his own, rather than together with Master Hand.

Master Hand and Crazy Hand have Stamina Bars like other bosses, rather than the usual HP shown at the bottom. Both Hands also suffer a much more severe HP drop than the other bosses, resulting in them having much less HP than the other bosses despite having above average HP in Classic Mode.

Galleom will be fought randomly in one of his two stages. His death animation will depend on when the player fights him. If they fight him as one of the earlier bosses, he will kneel to the ground, defeated (like his animation at the end of The Wilds I). If he is fought as one of the last three bosses before Tabuu, he will fall backwards to the ground (like his animation at the end of The Ruined Hall).

Additionally, while the attacks of bosses are normally slower in Boss Battles, Galleom's uppercut attack is always faster in Boss Battles than it is on the equivalent difficulty in the SSE.

The player can move while the Announcer is still saying "Ready?" and before he says "GO!".

Water effects from F.L.U.D.D. and Water Gun and Push effects from PSI Magnet will make the colour in the boss's health bar blink as it does when the boss takes damage, even though these moves inflict none.